About 50 of Australia's approximately 200 freshwater fish species occur in Victoria, and fish in Melbourne's rivers and creeks are typical of those in most Victorian coastal rivers They include 17 naturally occurring native species, with many more marine and estuarine species also present. These freshwater fish include eels, lampreys, galaxiids, gudgeons, blackfish, pygmy perch, smelt, grayling and tupong. Of these species, about 70% also have a marine phase to their life cycle, their eggs or larvae drifting into the estuary or sea, with young fish migrating back up the streams. A further three goby species, which are essentially estuarine, may also occur in the lower freshwater reaches. Barriers to fish passage caused by weirs have meant that many of these migratory species are no longer present in the upper reaches of Melbourne's rivers. As many fish in the Yarra River are migratory, the barrier at Dights Falls prevented access to the upstream river until the recent addition of a fish ladder.
In addition to native species, Melbourne's rivers also include a further 14 introduced native and exotic species. These are particularly prevalent in the Yarra River, giving it the most freshwater species of any river in Victoria. Many of the native species introduced to the area from outside their range are from northern waters, including Murray cod, Macquarie perch, golden perch, catfish and Australian bass.
The nine exotic fish species include carp, brown and rainbow trout, roach and redfin. Tench have been introduced for angling; weather loach and goldfish have probably been released from home aquariums, and Gambusia has been mistakenly introduced to control mosquitoes. The more hardy and tolerant of these exotic species now dominate some of the more degraded waterways. Threatened fish species include Macquarie perch, which has been translocated into the Yarra River to form a healthy population, the Australian grayling, the Yarra pygmy perch and the dwarf galaxias. Of the 19 freshwater species listed under Victoria's Flora and Fauna Guarantee Act 1988, seven are found in the Yarra River.